p_load(tidyverse)
remotes::install_github("federicomarini/GeneTonic",
dependencies = TRUE, build_vignettes = TRUE)
BiocManager::install("clusterProfiler")
BiocManager::install("pathview")
BiocManager::install("enrichplot")
library(clusterProfiler)
library(enrichplot)
p_load(biomaRt)
listMarts()
ensembl <- useMart("ensembl")
ensembl <- useDataset("hsapiens_gene_ensembl", mart = ensembl)
listDatasets(ensembl)
listAttributes(ensembl) %>% filter(! name %>% str_detect("homolog"))
searchAttributes(mart = ensembl, pattern = "GO")
genes
$by_area_stage
$by_area
NA
goids <- getBM(attributes = c('hgnc_symbol', 'description', 'name_1006', 'definition_1006', 'go_id','namespace_1003'),
filters = 'hgnc_symbol',
values = genes,
mart = ensembl)
goids %>% as_tibble %>% dplyr::select(hgnc_symbol, description, name_1006, definition_1006, go_id, namespace_1003) %>% filter(namespace_1003 %in% c("molecular_function", "biological_process"))
goids %>% count(name_1006) %>% arrange(desc(n))
goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE)
Categories with the word ‘transcription’
goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE) %>% count(name_1006)
goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE) %>%
ggplot() + geom_tile(aes(y = name_1006, x = as_factor(hgnc_symbol), fill = name_1006))
Radial glia: PFC: all marker genes
goids_x <- getBM(attributes = c('hgnc_symbol', 'description',
'name_1006', 'definition_1006', 'go_id',
'namespace_1003'),
filters = 'hgnc_symbol',
values = x,
mart = ensembl)
Error in martCheck(mart) : object 'ensembl' not found
dplyr::select(hgnc_symbol, name_1006, n, description, everything())
Error in dplyr::select(hgnc_symbol, name_1006, n, description, everything()) :
object 'hgnc_symbol' not found

tf_cofactors <- read_tsv("animalDB/Homo_sapiens_TF_cofactors.txt") %>% set_names(tolower(names(.)))
Parsed with column specification:
cols(
Species = col_character(),
Symbol = col_character(),
Ensembl = col_character(),
Family = col_character(),
`Entrez ID` = col_character()
)
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YWNlXzEwMDMsIHNjYWxlcyA9ICdmcmVlJykKYGBgCgoKCmBgYHtyfQp0ZnMgPC0gcmVhZF90YWJsZTIoImFuaW1hbERCL0hvbW9fc2FwaWVuc19URi50eHQiKSAlPiUgc2V0X25hbWVzKHRvbG93ZXIobmFtZXMoLikpKQoKbGVmdF9qb2luKHggJT4lIHRpYmJsZShzeW1ib2wgPSAuKSwgdGZzKSAlPiUgZmlsdGVyKCEgaXMubmEoZmFtaWx5KSkKCiMgNDMgZ2VuZXMgYXJlIGluIEFuaW1hbERCCmBgYAoKCmBgYHtyfQp0Zl9jb2ZhY3RvcnMgPC0gcmVhZF90c3YoImFuaW1hbERCL0hvbW9fc2FwaWVuc19URl9jb2ZhY3RvcnMudHh0IikgJT4lIHNldF9uYW1lcyh0b2xvd2VyKG5hbWVzKC4pKSkKCmxlZnRfam9pbih4ICU+JSB0aWJibGUoc3ltYm9sID0gLiksIHRmcykgJT4lIGZpbHRlcighIGlzLm5hKGZhbWlseSkpCgojIDQzIGdlbmVzIGFyZSBpbiBBbmltYWxEQgpgYGAKCgpgYGB7cn0KCmBgYAoK